molecular-dynamics

Molecular dynamics simulations for protein-ligand systems require systematic preparation, energy minimization, and NVT/NPT equilibration before production runs. This workflow uses OpenMM to set up the system and execute the simulation steps.

To calculate RMSD and RMSF from a trajectory, use MDAnalysis to process the output from your production run. This workflow supports trajectory analysis including RMSD, RMSF, contacts, and free energy surfaces.

OpenMM supports NVT and NPT equilibration for biomolecular simulations as part of the standard workflow. The process includes system preparation, energy minimization, equilibration, and subsequent production MD runs.

Setting up force fields for small-molecule MD simulations involves configuring parameters during the system preparation phase. This workflow supports force-field setup for both protein and small-molecule systems prior to minimization.

Conformational analysis and drug-binding studies can be performed using OpenMM and MDAnalysis. The workflow covers production MD runs and trajectory analysis to evaluate structural changes and interactions.

OpenMM and MDAnalysis are needed together because OpenMM executes the simulation and generates trajectories, while MDAnalysis processes these trajectories to compute RMSD, RMSF, contacts, and free energy surfaces.